Molecular Characterization of HIV-1 CRF01_AE in Mekong Delta, Vietnam, and Impact of T-Cell Epitope Mutations on HLA Recognition (ANRS 12159)

To date, 11 HIV-1 subtypes and 48 circulating recombinant forms have been described worldwide. The underlying reason why their distribution is so heterogeneous is not clear. Host genetic factors could partly explain this distribution. The aim of this study was to describe HIV-1 strains circulating in an unexplored area of Mekong Delta, Vietnam, and to assess the impact of optimal epitope mutations on HLA binding.We recruited 125 chronically antiretroviral-naive HIV-1-infected subjects from five cities in the Mekong Delta. We performed high-resolution DNA typing of HLA class I alleles, sequencing of Gag and RT-Prot genes and phylogenetic analysis of the strains. Epitope mutations were analyzed in patients bearing the HLA allele restricting the studied epitope. Optimal wild-type epitopes from the Los Alamos database were used as reference. T-cell epitope recognition was predicted using the immune epitope database tool according to three different scores involved in antigen processing (TAP and proteasome scores) and HLA binding (MHC score). with a Vietnamese specificity held by two different haplotypes. The percentage of homology between Mekong and B consensus HIV-1 sequences was above 85%. Divergent epitopes had TAP and proteasome scores comparable with wild-type epitopes. MHC scores were significantly lower in divergent epitopes with a mean of 2.4 (±0.9) versus 2 (±0.7) in non-divergent ones (p<0.0001).Our study confirms the wide predominance of CRF01_AE in the Mekong Delta where patients harbor a specific HLA pattern. Moreover, it demonstrates the lower MHC binding affinity among divergent epitopes. This weak immune pressure combined with a narrow genetic diversity favors immune escape and could explain why CRF01_AE is still predominant in Vietnam, particularly in the Mekong area

Drug resistance mutation (DRM) in RT sequences according to the international list of surveillance drug-resistance mutations (SDRMs) updated in 2009 [26].

<p>NVP = nevirapine, EFV = efavirenz, TDF = tenofovir, 3TC = lamivudine, ETV = etravirine.</p

Comparison of Gag (A) and RT (B) Vietnamese consensus sequences with HxB2 strains.

<p>Optimal CTL epitopes are highlighted by boxes. HLA restriction is indicated on the corresponding epitopes. Amino acid substitutions are indicated in bold. Shaded vertical bars separate blocks of 10 amino acids.</p

Proteasome, TAP and MHC score of CTL epitopes.

<p>Wild type epitope scores are matched with the corresponding divergent epitope score (Prot. score = proteasome score).</p>a<p>Epitopes for which amino acid divergence induces improved MHC binding.</p>b<p>Epitopes for which amino acid divergence decreases MHC binding.</p

Comparisons of proteasome, TAP and MHC scores between wild-type (B sub-type) and divergent epitopes (CRF01_AE sequences).

<p>All scores are logarithmic values, high values corresponding to highly predicted efficiency.</p

HLA allele frequencies in the Vietnamese Mekong Delta population (n = 116) compared to Kinh Vietnamese (dashed bars), Chinese (grey bars) and European (white bars) populations.

<p>The 6 most representative HLA alleles of the Mekong Delta population are represented.</p

Percentage of homology between CRF01_AE Vietnamese consensus sequences of RT, Prot and Gag aligned with the consensus CRF01_AE or B strain.

<p>Percentage of homology between CRF01_AE Vietnamese consensus sequences of RT, Prot and Gag aligned with the consensus CRF01_AE or B strain.</p

Phylogenic analysis of RT sequences of 125 Vietnamese HIV-1 patients.

<p>Phylogenic analysis of RT sequences of 125 Vietnamese HIV-1 patients.</p